# Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)

* [**10x scRNA-seq clustering analysis and annotation**](../notebooks/cluster_annotation_tutorial.ipynb):
  learn about the whole mouse brain taxonomy through some example use cases and
  visualization.
[*notebooks/cluster_annotation_tutorial.ipynb*]
* [**10x scRNA-seq gene expression data**](notebook_subtitle2.md): learn about
  the 10x dataset through some example use cases
* [**MERFISH whole brain spatial transcriptomics**](notebook_subtitle3.md):
  learn about the MERFISH dataset through some example use cases
* [**Cluster groups and embeddings**](../notebooks/cluster_groups_and_embeddings_tutorial.ipynb):
  learn about cell types neighborhoods and neighborhood specific UMAP
  embeddings through example use cases.
[*notebooks/cluster_groups_and_embeddings_tutorial.ipynb*]
* [**Cell type neighborhood gallery**](../notebooks/cluster_neighborhood_gallery.ipynb):
  explore and visualize a set of cell types neighborhoods.
[*notebooks/cluster_neighborhood_gallery.ipynb*]
* [**Allen CCFv3 parcellation and annotation**](../notebooks/ccf_and_parcellation_annotation_tutorial.ipynb):
  learn about the Allen CCFv3 and a simplified 5-level anatomical hierarchy
  through some example use cases and visualization.
[*notebooks/ccf_and_parcellation_annotation_tutorial.ipynb*]
* [**MERFISH CCF mapped coordinates**](../notebooks/merfish_ccf_registration_tutorial.ipynb):
  learn about how to download and use CCF mapped coordinates through some
  example use cases and visualization.
[*notebooks/merfish_ccf_registration_tutorial.ipynb*]